Just short addition to Pavel's description.
To stably simulate RNA and DNA, it was necessary to prepare
separate chi dihedral parameters for RNA and DNA,
i.e., chiOL3 and chiOL4.
It is described in the original papers and some recent reviews.
Jiri
On Mon, 29 Dec 2014, pavel.banas.upol.cz wrote:
> Date: Mon, 29 Dec 2014 17:32:13 +0100 (CET)
> From: pavel.banas.upol.cz
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] amber force field
>
> Hi Jane,
> currently the best performing and widely tested force field version for RNAs
> is (ff99 + bsc0 + χOL3), which is also AMBER default, see e.g. first
> (comment) line of parm10.dat file.
>
> have a nice day and all the best in 2015,
>
> Pavel
>
> --
> Pavel Banáš
> pavel.banas.upol.cz
> Department of Physical Chemistry,
> Palacky University Olomouc
> Czech Republic
>
>
>
> ---------- Původní zpráva ----------
> Od: 王珍 <wangzhenzk.126.com>
> Komu: amber.ambermd.org <amber.ambermd.org>
> Datum: 28. 12. 2014 12:54:14
> Předmět: [AMBER] amber force field
>
> "Hi all,I have seen you sent the force field (ff99 + bsc0 + ε/ζOL1+ χOL4)
> for DNA. I want to use the nearest modified force field to computate the
> RNA. Could you give me the nearest modified force field(ff99 + bsc0 + ε/ζOL1
> + χOL4) for RNA? Thank you inadvance.With kind regards,Jane
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Received on Tue Dec 30 2014 - 01:30:02 PST
